Background: Most clinical isolates of Vibrio parahaemolyticus produce a major virulence factor known as the thermostable direct hemolysin (TDH). TDH is encoded by the tdh gene which is located in a genomic pathogenicity island (PAI). Most environmental isolates are described as tdh negative. Aim: To assess if environmental strains lack the full pathogenicity island or if only the tdh gene is deleted. Material and methods: Thirty eight clinical and 66 environmental strains of Vibrio parahaemolyticus were studied. PAI was characterized by polymerase chain reaction (PCR). The presence of tdhA and tdhS genes, was determined by Southern blot. Results: Fifty three environmental strains (80%) lacked a full PAI when compared with clinical strains. In environmental strains, Southern blot and sequence analysis showed that a genetic región of 80 kilobase pairs including genes from VPA1310 to VPA1396 was missing. Conclusions: These results highlight the genetic dynamism of Vibrio parahaemolyticus pathogenecity island región and suggest that new pathogenic strains could appear by horizontal transfer of the island between toxigenic and non-toxigenic strains.